Molecular Plant Breeding 2016, Vol.7, No.28, 1
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HSY regions and differs from each other by only 0.4% sequences. Three different populations of Y chromosomes
(MSY1, MSY2, and MSY3) were identified from wild papaya males. Findings revealed that the MSY1 and
MSY2 haplotype groups were found from the two opposite coasts of Costa Rica. Third population of Y
chromosome i.e. MSY3 as well as all HSY haplotype groups were identified from the north Pacific region of
Costa Rica.
3.8 Sex-specific repeats
The sex chromosomes of papaya contain sex specific repeats. Twenty HSY-specific and one X-specific repeats
were identified. The portion of HSY in which expansion occurs, contains HSY-specific repeats (from 2.0 to 4.0
and 5.0 to 7.5 Mb). Expansion in HSY occurs mostly due to accumulation of these sex-specific repeats. Both X
and HSY possess highest amount of repeat Ty3-gypsy retrotransposons. X region contains 67.2% repetitive
element, which is lower than HSY and Y chromosome. The importance of HSY and X-specific repeats may be in
developing the molecular markers specific for sex identification (Na et al., 2014).
3.9 Role of sRNAs in sex determination
Aryal et al. (2014) analyzed small non-coding RNAs (sRNA) in the libraries prepared from female, male and
hermaphrodite flowers of papaya. sRNA plays an significant role in gene silencing and DNA methylation,
suggesting its involvement in sex differentiation in plants. lllumina libraries were made from the floral male, female,
and hermaphrodite papaya plants for the study of sRNA reads. A total of 29 micro RNAs (miRNAs) were detected
using these sRNA reads. In one library, a total of 65 miRNAs (34 new and 31 conserved miRNAs) were identified.
From these miRNAs, only 14 miRNAswere differentially expressed among male, female and hermaphrodite
flowers. Six miRNAs (miR160, miR167a, miR167b, miR169 and miR393) were expressed higher in papaya male
flowers that regulate the genes in auxin signaling pathway which indicates that auxin plays a main role in carpel
development. Two miRNAs (miR159 and miR166) were expressed higher in female flowers, which played an
important role in regulating the genes responsible for floral meristem identity and the embryo patterning. Four
miRNAs (miR156a, miR156b, miR168b and miR_novel_39) were expressed higher in hermaphrodite and male
flowers. Two miRNAs (miR171 and miR394) were expressed higher in female and male flowers. The results
indicate potential role of these sRNAs in papaya sex determination.
4 Papaya Genome Sequencing
A draft genome sequence of papaya was generated from a SunUP female plant using the whole-genome shotgun
approach with Sanger method. It was assembled into 271Mb contigs and unassembled portion may contain
repetitive sequences. Papaya genome contains 24,476 genes with average gene length 2,373 bp. Total 35.5% GC
content is present in the genome and average intron length is 479 bp (Ming et al., 2008). Papaya genome sequences
could be is a valuable source to study the mechanism of sex determination at molecular level.
5 Methods for Identification of Sex Types
Papaya sex identification at early plant development stage has been a problem since long back which led to the
researchers to develop many marker techniques such as, (1) morphology based, (2) biochemical markers, (3)
polymerase chain reaction (PCR)-based markers and (4) sequencing-based markers (Figure 3). Morphological
methods differentiate the sex types on the basis of traits such as leaf or root morphology, rate of growth and seed
coat color etc. (Reddy et al., 2012; Demandante et al., 2014). Several other cytological methods (Datta, 1971) and
Isozyme (biochemical) markers have been used for sex type identification (Sriprasertsak et al., 1988). Molecular
markers are divided into two types (i) PCR-based molecular markers and (ii) sequence-based molecular markers.
PCR based molecular markers includes: (a) Random amplified polymorphic DNA (RAPD), (b) AFLP, (c) Inter
simple sequence repeat (ISSR), and sequence-based molecular markers includes (a) simple sequence repeats
(SSR), and (b) single nucleotide polymorphism (SNP).
